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- EMDB-24323: T-Plastin-F-actin complex -

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Basic information

Entry
Database: EMDB / ID: EMD-24323
TitleT-Plastin-F-actin complex
Map data
Sample
  • Complex: T-Plastin-F-actin complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Plastin-3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION
Function / homology
Function and homology information


actin filament network formation / Striated Muscle Contraction / actin filament bundle / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement ...actin filament network formation / Striated Muscle Contraction / actin filament bundle / actin filament bundle assembly / skeletal muscle thin filament assembly / striated muscle thin filament / skeletal muscle fiber development / stress fiber / actin filament / Hydrolases; Acting on acid anhydrides; Acting on acid anhydrides to facilitate cellular and subcellular movement / bone development / actin filament binding / hydrolase activity / calcium ion binding / ATP binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Fimbrin/Plastin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Actins signature 1. ...Fimbrin/Plastin / Actinin-type actin-binding domain signature 1. / Actinin-type actin-binding domain signature 2. / Actinin-type actin-binding domain, conserved site / Calponin homology domain / Calponin homology (CH) domain / Calponin homology domain / CH domain superfamily / Calponin homology (CH) domain profile. / Actins signature 1. / Actin, conserved site / Actins signature 2. / Actin/actin-like conserved site / Actins and actin-related proteins signature. / Actin / Actin family / Actin / EF-hand domain pair / EF-hand, calcium binding motif / ATPase, nucleotide binding domain / EF-Hand 1, calcium-binding site / EF-hand calcium-binding domain. / EF-hand calcium-binding domain profile. / EF-hand domain / EF-hand domain pair
Similarity search - Domain/homology
Plastin-3 / Actin, alpha skeletal muscle
Similarity search - Component
Biological speciesHomo sapiens (human) / Chicken (chicken)
Methodhelical reconstruction / cryo EM / Resolution: 2.6 Å
AuthorsMei L / Alushin GM
Funding support United States, 2 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of Dental and Craniofacial Research (NIH/NIDCR)5DP5OD017885 United States
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R01GM141044 United States
CitationJournal: Proc Natl Acad Sci U S A / Year: 2022
Title: Structural mechanism for bidirectional actin cross-linking by T-plastin.
Authors: Lin Mei / Matthew J Reynolds / Damien Garbett / Rui Gong / Tobias Meyer / Gregory M Alushin /
Abstract: To orchestrate cell mechanics, trafficking, and motility, cytoskeletal filaments must assemble into higher-order networks whose local subcellular architecture and composition specify their functions. ...To orchestrate cell mechanics, trafficking, and motility, cytoskeletal filaments must assemble into higher-order networks whose local subcellular architecture and composition specify their functions. Cross-linking proteins bridge filaments at the nanoscale to control a network's μm-scale geometry, thereby conferring its mechanical properties and functional dynamics. While these interfilament linkages are key determinants of cytoskeletal function, their structural mechanisms remain poorly understood. Plastins/fimbrins are an evolutionarily ancient family of tandem calponin-homology domain (CHD) proteins required to construct multiple classes of actin networks, which feature diverse geometries specialized to power cytokinesis, microvilli and stereocilia biogenesis, and persistent cell migration. Here, we focus on the structural basis of actin network assembly by human T-plastin, a ubiquitously expressed isoform necessary for the maintenance of stable cellular protrusions generated by actin polymerization forces. By implementing a machine-learning-enabled cryo-electron microscopy pipeline for visualizing cross-linkers bridging multiple filaments, we uncover a sequential bundling mechanism enabling T-plastin to bridge pairs of actin filaments in both parallel and antiparallel orientations. T-plastin populates distinct structural landscapes in these two bridging orientations that are selectively compatible with actin networks featuring divergent architectures and functions. Our structural, biochemical, and cell biological data highlight inter-CHD linkers as key structural elements underlying flexible but stable cross-linking that are likely to be disrupted by T-plastin mutations that cause hereditary bone diseases.
History
DepositionJun 28, 2021-
Header (metadata) releaseJul 6, 2022-
Map releaseJul 6, 2022-
UpdateSep 21, 2022-
Current statusSep 21, 2022Processing site: RCSB / Status: Released

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Structure visualization

Supplemental images

emd_24323.png

Downloads & links

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Map

FileDownload / File: emd_24323.map.gz / Format: CCP4 / Size: 12 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
Voxel sizeX=Y=Z: 1.06 Å
Density
Contour LevelBy AUTHOR: 0.03
Minimum - Maximum-0.1349161 - 0.44294873
Average (Standard dev.)0.003829898 (±0.021143477)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderZYX
Origin192127188
Dimensions137180128
Spacing128137180
CellA: 135.68 Å / B: 145.21999 Å / C: 190.79999 Å
α=β=γ: 90.0 °

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Supplemental data

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Mask #1

Fileemd_24323_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: unsharpened, unfiltered map from 3d auto-refinement

Fileemd_24323_additional_1.map
Annotationunsharpened, unfiltered map from 3d auto-refinement
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Additional map: full, sharpened, local resolution-filtered map

Fileemd_24323_additional_2.map
Annotationfull, sharpened, local resolution-filtered map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #1

Fileemd_24323_half_map_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Half map: #2

Fileemd_24323_half_map_2.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

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Sample components

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Entire : T-Plastin-F-actin complex

EntireName: T-Plastin-F-actin complex
Components
  • Complex: T-Plastin-F-actin complex
    • Protein or peptide: Actin, alpha skeletal muscle
    • Protein or peptide: Plastin-3
  • Ligand: ADENOSINE-5'-DIPHOSPHATE
  • Ligand: MAGNESIUM ION

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Supramolecule #1: T-Plastin-F-actin complex

SupramoleculeName: T-Plastin-F-actin complex / type: complex / ID: 1 / Parent: 0 / Macromolecule list: #1-#2
Details: Full-length human T-Plastin (PLS3) bound to F-actin in the presence of calcium
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 27.5 kDa/nm

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Macromolecule #1: Actin, alpha skeletal muscle

MacromoleculeName: Actin, alpha skeletal muscle / type: protein_or_peptide / ID: 1 / Number of copies: 5 / Enantiomer: LEVO
Source (natural)Organism: Chicken (chicken)
Molecular weightTheoretical: 42.109973 KDa
SequenceString: MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY ...String:
MCDEDETTAL VCDNGSGLVK AGFAGDDAPR AVFPSIVGRP RHQGVMVGMG QKDSYVGDEA QSKRGILTLK YPIE(HIC)G IIT NWDDMEKIWH HTFYNELRVA PEEHPTLLTE APLNPKANRE KMTQIMFETF NVPAMYVAIQ AVLSLYASGR TTGIVLD SG DGVTHNVPIY EGYALPHAIM RLDLAGRDLT DYLMKILTER GYSFVTTAER EIVRDIKEKL CYVALDFENE MATAASSS S LEKSYELPDG QVITIGNERF RCPETLFQPS FIGMESAGIH ETTYNSIMKC DIDIRKDLYA NNVMSGGTTM YPGIADRMQ KEITALAPST MKIKIIAPPE RKYSVWIGGS ILASLSTFQQ MWITKQEYDE AGPSIVHRKC F

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Macromolecule #2: Plastin-3

MacromoleculeName: Plastin-3 / type: protein_or_peptide / ID: 2 / Number of copies: 3 / Enantiomer: LEVO
Source (natural)Organism: Homo sapiens (human)
Molecular weightTheoretical: 70.896867 KDa
Recombinant expressionOrganism: Escherichia coli (E. coli)
SequenceString: MDEMATTQIS KDELDELKEA FAKVDLNSNG FICDYELHEL FKEANMPLPG YKVREIIQKL MLDGDRNKDG KISFDEFVYI FQEVKSSDI AKTFRKAINR KEGICALGGT SELSSEGTQH SYSEEEKYAF VNWINKALEN DPDCRHVIPM NPNTDDLFKA V GDGIVLCK ...String:
MDEMATTQIS KDELDELKEA FAKVDLNSNG FICDYELHEL FKEANMPLPG YKVREIIQKL MLDGDRNKDG KISFDEFVYI FQEVKSSDI AKTFRKAINR KEGICALGGT SELSSEGTQH SYSEEEKYAF VNWINKALEN DPDCRHVIPM NPNTDDLFKA V GDGIVLCK MINLSVPDTI DERAINKKKL TPFIIQENLN LALNSASAIG CHVVNIGAED LRAGKPHLVL GLLWQIIKIG LF ADIELSR NEALAALLRD GETLEELMKL SPEELLLRWA NFHLENSGWQ KINNFSADIK DSKAYFHLLN QIAPKGQKEG EPR IDINMS GFNETDDLKR AESMLQQADK LGCRQFVTPA DVVSGNPKLN LAFVANLFNK YPALTKPENQ DIDWTLLEGE TREE RTFRN WMNSLGVNPH VNHLYADLQD ALVILQLYER IKVPVDWSKV NKPPYPKLGA NMKKLENCNY AVELGKHPAK FSLVG IGGQ DLNDGNQTLT LALVWQLMRR YTLNVLEDLG DGQKANDDII VNWVNRTLSE AGKSTSIQSF KDKTISSSLA VVDLID AIQ PGCINYDLVK SGNLTEDDKH NNAKYAVSMA RRIGARVYAL PEDLVEVKPK MVMTVFACLM GRGMKRV

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Macromolecule #3: ADENOSINE-5'-DIPHOSPHATE

MacromoleculeName: ADENOSINE-5'-DIPHOSPHATE / type: ligand / ID: 3 / Number of copies: 5 / Formula: ADP
Molecular weightTheoretical: 427.201 Da
Chemical component information

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM / Adenosine diphosphate

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Macromolecule #4: MAGNESIUM ION

MacromoleculeName: MAGNESIUM ION / type: ligand / ID: 4 / Number of copies: 5 / Formula: MG
Molecular weightTheoretical: 24.305 Da

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Experimental details

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Structure determination

Methodcryo EM
Processinghelical reconstruction
Aggregation statehelical array

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Sample preparation

BufferpH: 7.5
VitrificationCryogen name: ETHANE

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Electron microscopy

MicroscopeFEI TITAN KRIOS
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsIllumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELDBright-field microscopy
Image recordingFilm or detector model: GATAN K2 SUMMIT (4k x 4k) / Detector mode: COUNTING / Digitization - Frames/image: 1-50 / Number grids imaged: 1 / Average exposure time: 10.0 sec. / Average electron dose: 71.02 e/Å2
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

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Image processing

Segment selectionNumber selected: 577659 / Software - Name: RELION (ver. 3.1) / Details: helical auto-picking
CTF correctionSoftware - Name: CTFFIND (ver. 4.0)
Startup modelType of model: EMDB MAP
EMDB ID:

20843

Final angle assignmentType: NOT APPLICABLE / Software - Name: RELION (ver. 3.1)
Final reconstructionApplied symmetry - Helical parameters - Δz: 27.4 Å
Applied symmetry - Helical parameters - Δ&Phi: -166.8 °
Applied symmetry - Helical parameters - Axial symmetry: C1 (asymmetric)
Resolution.type: BY AUTHOR / Resolution: 2.6 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: RELION (ver. 3.1) / Number images used: 442523
FSC plot (resolution estimation)

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Atomic model buiding 1

Initial modelPDB ID:

6upv


Chain - Chain ID: A
Output model

PDB-7r94:
T-Plastin-F-actin complex

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